Oncomine 3.0: Genes, Pathways, and Networks in a Collection of 18,000 Cancer Gene Expression Profiles

Neoplasia. 2007 Feb;9(2):166-80. doi: 10.1593/neo.07112.

Abstract

DNA microarrays have been widely applied to cancer transcriptome analysis; however, the majority of such data are not easily accessible or comparable. Furthermore, several important analytic approaches have been applied to microarray analysis; however, their application is often limited. To overcome these limitations, we have developed Oncomine, a bioinformatics initiative aimed at collecting, standardizing, analyzing, and delivering cancer transcriptome data to the biomedical research community. Our analysis has identified the genes, pathways, and networks deregulated across 18,000 cancer gene expression microarrays, spanning the majority of cancer types and subtypes. Here, we provide an update on the initiative, describe the database and analysis modules, and highlight several notable observations. Results from this comprehensive analysis are available at http://www.oncomine.org.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Antineoplastic Agents / pharmacology
  • Chromosome Mapping
  • Chromosomes, Human / genetics
  • Computational Biology / organization & administration*
  • Data Collection
  • Data Display
  • Data Interpretation, Statistical
  • Databases, Genetic*
  • Drug Design
  • Electronic Data Processing
  • Gene Expression Profiling* / statistics & numerical data
  • Gene Expression Regulation, Neoplastic*
  • Genes, Neoplasm*
  • Humans
  • Internet
  • Models, Biological
  • Neoplasm Proteins / biosynthesis
  • Neoplasm Proteins / chemistry
  • Neoplasm Proteins / genetics*
  • Neoplasms / classification
  • Neoplasms / genetics
  • Neoplasms / metabolism
  • Oligonucleotide Array Sequence Analysis*
  • Subtraction Technique
  • Transcription, Genetic

Substances

  • Antineoplastic Agents
  • Neoplasm Proteins